Variant report

Variant	rs793446
Chromosome Location	chr3:99578114-99578115
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:99565953..99568570-chr3:99576514..99579322,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168386	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11719468	0.85[CEU][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs1287284	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13059754	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1384062	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1610509	0.88[JPT][hapmap]
rs16841874	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs1718235	0.84[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.80[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2638948	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35422475	0.81[AMR][1000 genomes]
rs4577503	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4928150	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4928151	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4928230	0.84[CEU][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs4928235	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4928237	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs58704213	0.81[ASN][1000 genomes]
rs6440967	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs6806323	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs704571	0.88[JPT][hapmap]
rs704572	0.92[JPT][hapmap]
rs704574	0.88[JPT][hapmap]
rs7613864	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7649349	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs7650727	0.84[CEU][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs766778	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs792831	0.88[JPT][hapmap]
rs792835	0.88[JPT][hapmap]
rs792836	0.88[JPT][hapmap]
rs792837	0.88[JPT][hapmap]
rs793437	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs793439	0.84[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs793443	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793456	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs793464	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs793475	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs793476	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs793483	0.88[JPT][hapmap]
rs793485	0.88[JPT][hapmap]
rs793497	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs793502	0.83[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs796976	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs813218	0.84[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs902159	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs923472	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs793446	C3orf26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99537200-99594400	Weak transcription	Esophagus	oesophagus
2	chr3:99538200-99584600	Weak transcription	Primary T cells from cord blood	blood
3	chr3:99562600-99578200	Weak transcription	Fetal Kidney	kidney
4	chr3:99562800-99580200	Weak transcription	Gastric	stomach
5	chr3:99563200-99593600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:99565200-99585000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr3:99565600-99584800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:99565600-99589400	Weak transcription	K562	blood
9	chr3:99566000-99578400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:99567800-99581600	Weak transcription	Spleen	Spleen
11	chr3:99568000-99578600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr3:99568000-99580000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:99569000-99589600	Weak transcription	Colonic Mucosa	Colon
14	chr3:99569800-99579200	Weak transcription	Right Ventricle	heart
15	chr3:99569800-99579400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:99569800-99580200	Weak transcription	Lung	lung
17	chr3:99570400-99579200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:99570400-99579200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr3:99570600-99581600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:99571000-99579200	Enhancers	Rectal Smooth Muscle	rectum
21	chr3:99571000-99579400	Enhancers	Colon Smooth Muscle	Colon
22	chr3:99573000-99580400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr3:99573200-99594000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr3:99573400-99589200	Genic enhancers	HepG2	liver
25	chr3:99573600-99584800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr3:99574000-99579400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:99574000-99584000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr3:99574200-99578800	Weak transcription	Fetal Intestine Small	intestine
29	chr3:99574400-99590000	Weak transcription	Liver	Liver
30	chr3:99574800-99578200	Enhancers	Muscle Satellite Cultured Cells	--
31	chr3:99575000-99580200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr3:99575000-99587000	Weak transcription	Pancreas	Pancrea
33	chr3:99575000-99593600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr3:99575200-99579000	Weak transcription	Small Intestine	intestine
35	chr3:99575200-99587000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:99575400-99579200	Weak transcription	Psoas Muscle	Psoas
37	chr3:99575400-99582000	Weak transcription	GM12878-XiMat	blood
38	chr3:99575600-99581000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:99575800-99578200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:99575800-99580000	Weak transcription	Placenta	Placenta
41	chr3:99576000-99579400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:99576000-99587600	Genic enhancers	NHDF-Ad	bronchial
43	chr3:99576400-99585000	Weak transcription	A549	lung
44	chr3:99576600-99578200	Weak transcription	Stomach Mucosa	stomach
45	chr3:99577000-99578400	Weak transcription	Adipose Nuclei	Adipose
46	chr3:99577200-99578200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:99577200-99578200	Strong transcription	Duodenum Mucosa	Duodenum
48	chr3:99577400-99578200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:99577400-99578200	Genic enhancers	Aorta	Aorta
50	chr3:99577400-99578200	Strong transcription	Ovary	ovary

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